| Chain sequence(s) |
B: ATDKLSTQWNILYHLGGNGPWIPKIEGVVDGGIAIPNGCKIDMIHMMSRHGERYPTQNAGERMIALVERIKSNGREMRGALTFMNHWDYFSHAEQLTTTGPYAGTLEAFGTGVKFRTRYHHLWNDTTLHPPPTLFWASEADRVVDTAKYFGAGFFGLDYEQSAKLEIISEAADKGGNTLTPGDTCTKYLEDLETGRILGEQMLFKYRSTYLPAIAKRLEEENPGFEFTDSEIYSMQEMCGFETTVRGSSKWCNVFTQDEWLKFEYARDVIHFYRAGPGNPYAMAMGWLWLNATANLIQKGPEAGPVFLSFGHDGDIIPMLAALGLFDDEKKLPTDEVYTNRRWRTSQIVPMGGRILLQRMVCSADPSHDSQAGVFIRFNVNDGIVALPGCDSGPGESCPLDRLMAHVAERGSMGGDFRKTCGLPEWAPDRLTFLRQP
input PDB |
| Selected Chain(s) | B |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| alphaCutter usage | No |
| Dynamic mode | No |
| Automated mutations | No |
| Downloads | Download all the data |
| Simulation log |
[INFO] Logger: Verbosity set to: 2 - [INFO] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with B chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:12:52)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/9dd7144dc45722b/tmp/folded.pdb (00:12:52)
[INFO] Main: Simulation completed successfully. (00:20:45)
|
The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan4D score | mutation |
|---|---|---|---|---|
| 14 | A | B | -0.6379 | |
| 15 | T | B | -1.1722 | |
| 16 | D | B | -2.2818 | |
| 17 | K | B | -1.8928 | |
| 18 | L | B | 0.1692 | |
| 19 | S | B | -0.1237 | |
| 20 | T | B | 0.0253 | |
| 21 | Q | B | -0.0143 | |
| 22 | W | B | 0.5513 | |
| 23 | N | B | -0.1482 | |
| 24 | I | B | 0.2837 | |
| 25 | L | B | 0.2357 | |
| 26 | Y | B | 0.0000 | |
| 27 | H | B | 0.0000 | |
| 28 | L | B | 0.0000 | |
| 29 | G | B | 0.0000 | |
| 30 | G | B | 0.0000 | |
| 31 | N | B | -0.1137 | |
| 32 | G | B | 0.0000 | |
| 33 | P | B | 0.0774 | |
| 34 | W | B | 0.1730 | |
| 35 | I | B | 0.1783 | |
| 36 | P | B | -0.3218 | |
| 37 | K | B | 0.0000 | |
| 38 | I | B | -0.6626 | |
| 39 | E | B | -1.1838 | |
| 40 | G | B | -0.1623 | |
| 41 | V | B | 1.3526 | |
| 42 | V | B | 1.3341 | |
| 43 | D | B | -0.6783 | |
| 44 | G | B | -0.1932 | |
| 45 | G | B | 0.1035 | |
| 46 | I | B | 0.6133 | |
| 47 | A | B | 0.0897 | |
| 48 | I | B | -0.0690 | |
| 49 | P | B | -1.0227 | |
| 50 | N | B | -1.6974 | |
| 51 | G | B | -1.1783 | |
| 52 | C | B | 0.0000 | |
| 53 | K | B | -1.7774 | |
| 54 | I | B | 0.0000 | |
| 55 | D | B | -1.4946 | |
| 56 | M | B | 0.0000 | |
| 57 | I | B | 0.0000 | |
| 58 | H | B | 0.0000 | |
| 59 | M | B | 0.0000 | |
| 60 | M | B | 0.0000 | |
| 61 | S | B | 0.0000 | |
| 62 | R | B | 0.0000 | |
| 63 | H | B | 0.0000 | |
| 64 | G | B | 0.0000 | |
| 65 | E | B | 0.0000 | |
| 66 | R | B | -0.0292 | |
| 67 | Y | B | -0.2340 | |
| 68 | P | B | 0.0000 | |
| 69 | T | B | -1.4014 | |
| 70 | Q | B | -2.7961 | |
| 71 | N | B | -2.5075 | |
| 72 | A | B | 0.0000 | |
| 73 | G | B | 0.0000 | |
| 74 | E | B | -2.6981 | |
| 75 | R | B | -1.6458 | |
| 76 | M | B | 0.0000 | |
| 77 | I | B | -0.5538 | |
| 78 | A | B | -1.1784 | |
| 79 | L | B | -1.3318 | |
| 80 | V | B | 0.0000 | |
| 81 | E | B | -2.8660 | |
| 82 | R | B | -3.2218 | |
| 83 | I | B | 0.0000 | |
| 84 | K | B | -3.6023 | |
| 85 | S | B | -3.0891 | |
| 86 | N | B | -3.1196 | |
| 87 | G | B | -2.4908 | |
| 88 | R | B | -3.3532 | |
| 89 | E | B | -3.2234 | |
| 90 | M | B | -2.3295 | |
| 91 | R | B | -3.0198 | |
| 92 | G | B | -1.7239 | |
| 93 | A | B | -1.3118 | |
| 94 | L | B | 0.0000 | |
| 95 | T | B | -1.4219 | |
| 96 | F | B | -1.1407 | |
| 97 | M | B | -1.5214 | |
| 98 | N | B | -1.8770 | |
| 99 | H | B | -1.6061 | |
| 100 | W | B | -1.3455 | |
| 101 | D | B | -1.8746 | |
| 102 | Y | B | -0.5509 | |
| 103 | F | B | -0.6379 | |
| 104 | S | B | -0.9720 | |
| 105 | H | B | -1.5774 | |
| 106 | A | B | -1.5953 | |
| 112 | E | B | -2.9398 | |
| 113 | Q | B | -2.2461 | |
| 114 | L | B | -1.2608 | |
| 115 | T | B | -1.6421 | |
| 116 | T | B | -1.1325 | |
| 117 | T | B | -0.6648 | |
| 118 | G | B | -0.2288 | |
| 119 | P | B | 0.0000 | |
| 120 | Y | B | 1.4598 | |
| 121 | A | B | 0.8657 | |
| 122 | G | B | 0.0000 | |
| 123 | T | B | 1.0341 | |
| 124 | L | B | 2.1529 | |
| 125 | E | B | 1.0333 | |
| 126 | A | B | 0.0000 | |
| 127 | F | B | 1.4285 | |
| 128 | G | B | 0.6069 | |
| 129 | T | B | 0.0000 | |
| 130 | G | B | 0.0000 | |
| 131 | V | B | -0.1371 | |
| 132 | K | B | -1.5825 | |
| 133 | F | B | 0.0000 | |
| 134 | R | B | -1.5320 | |
| 135 | T | B | -1.5061 | |
| 136 | R | B | -1.9358 | |
| 137 | Y | B | 0.0000 | |
| 138 | H | B | -1.7686 | |
| 139 | H | B | -1.9589 | |
| 140 | L | B | 0.0000 | |
| 141 | W | B | 0.0000 | |
| 142 | N | B | -1.8764 | |
| 143 | D | B | -1.3133 | |
| 144 | T | B | -0.5534 | |
| 145 | T | B | -0.1278 | |
| 146 | L | B | -0.0613 | |
| 147 | H | B | 0.0000 | |
| 148 | P | B | -1.0253 | |
| 149 | P | B | -0.8123 | |
| 150 | P | B | -1.2456 | |
| 151 | T | B | -0.6283 | |
| 152 | L | B | -0.6424 | |
| 153 | F | B | 0.0000 | |
| 154 | W | B | 0.0000 | |
| 155 | A | B | 0.0000 | |
| 156 | S | B | 0.0000 | |
| 157 | E | B | -2.1542 | |
| 158 | A | B | -1.9310 | |
| 159 | D | B | -2.5662 | |
| 160 | R | B | -1.8896 | |
| 161 | V | B | 0.0000 | |
| 162 | V | B | -1.3276 | |
| 163 | D | B | -1.7134 | |
| 164 | T | B | 0.0000 | |
| 165 | A | B | 0.0000 | |
| 166 | K | B | -0.8758 | |
| 167 | Y | B | 0.4943 | |
| 168 | F | B | 0.0000 | |
| 169 | G | B | 0.0000 | |
| 170 | A | B | 0.2620 | |
| 171 | G | B | 0.0000 | |
| 172 | F | B | 0.0000 | |
| 173 | F | B | 0.0000 | |
| 174 | G | B | 0.6804 | |
| 175 | L | B | 1.1029 | |
| 176 | D | B | 0.0000 | |
| 177 | Y | B | -0.9669 | |
| 178 | E | B | -2.3048 | |
| 179 | Q | B | -2.2046 | |
| 180 | S | B | 0.0000 | |
| 183 | A | B | -1.5804 | |
| 184 | K | B | -1.9641 | |
| 185 | L | B | -0.4725 | |
| 186 | E | B | -0.1541 | |
| 187 | I | B | 0.2120 | |
| 188 | I | B | 0.0000 | |
| 189 | S | B | -1.2112 | |
| 190 | E | B | -1.5036 | |
| 191 | A | B | -1.2880 | |
| 192 | A | B | -1.2194 | |
| 193 | D | B | -1.9758 | |
| 194 | K | B | -1.7457 | |
| 195 | G | B | 0.0000 | |
| 196 | G | B | 0.0000 | |
| 197 | N | B | -1.2523 | |
| 198 | T | B | 0.0000 | |
| 199 | L | B | 0.0000 | |
| 200 | T | B | -0.6305 | |
| 201 | P | B | -0.5355 | |
| 202 | G | B | -0.5852 | |
| 203 | D | B | 0.0000 | |
| 204 | T | B | -0.4250 | |
| 205 | C | B | -0.7907 | |
| 206 | T | B | -1.3998 | |
| 207 | K | B | -1.7763 | |
| 208 | Y | B | -1.0519 | |
| 209 | L | B | 0.0000 | |
| 210 | E | B | -3.2398 | |
| 211 | D | B | -2.3012 | |
| 212 | L | B | -1.9575 | |
| 213 | E | B | -2.2051 | |
| 214 | T | B | -0.6879 | |
| 215 | G | B | -1.2475 | |
| 216 | R | B | -2.6643 | |
| 217 | I | B | 0.0000 | |
| 218 | L | B | 0.2784 | |
| 219 | G | B | -1.6586 | |
| 220 | E | B | -2.4447 | |
| 221 | Q | B | -1.2752 | |
| 222 | M | B | 0.0829 | |
| 223 | L | B | 1.8115 | |
| 224 | F | B | 1.6401 | |
| 225 | K | B | 0.3397 | |
| 226 | Y | B | 0.1822 | |
| 227 | R | B | -0.5445 | |
| 228 | S | B | -0.9561 | |
| 229 | T | B | -0.6426 | |
| 230 | Y | B | -0.2412 | |
| 231 | L | B | 0.0000 | |
| 232 | P | B | -0.8506 | |
| 233 | A | B | -1.1341 | |
| 234 | I | B | 0.0000 | |
| 235 | A | B | 0.0000 | |
| 236 | K | B | -3.5570 | |
| 237 | R | B | -3.5784 | |
| 238 | L | B | 0.0000 | |
| 239 | E | B | -3.2785 | |
| 240 | E | B | -4.0615 | |
| 241 | E | B | -3.2974 | |
| 242 | N | B | 0.0000 | |
| 243 | P | B | -2.5221 | |
| 244 | G | B | -2.2744 | |
| 245 | F | B | 0.0000 | |
| 246 | E | B | -2.7642 | |
| 247 | F | B | 0.0000 | |
| 248 | T | B | -1.0969 | |
| 249 | D | B | -0.6079 | |
| 250 | S | B | -0.1566 | |
| 251 | E | B | 0.0000 | |
| 252 | I | B | 0.0000 | |
| 253 | Y | B | 0.0000 | |
| 254 | S | B | 0.0000 | |
| 255 | M | B | 0.0000 | |
| 256 | Q | B | 0.0000 | |
| 257 | E | B | 0.0000 | |
| 258 | M | B | 0.0000 | |
| 259 | C | B | 0.0000 | |
| 260 | G | B | 0.0000 | |
| 261 | F | B | 0.0000 | |
| 262 | E | B | 0.0000 | |
| 263 | T | B | -0.9767 | |
| 264 | T | B | 0.0000 | |
| 265 | V | B | -0.4629 | |
| 266 | R | B | -1.8237 | |
| 267 | G | B | -1.4212 | |
| 268 | S | B | -1.5055 | |
| 269 | S | B | -1.6209 | |
| 270 | K | B | -2.0439 | |
| 271 | W | B | 0.0000 | |
| 272 | C | B | -1.1026 | |
| 273 | N | B | -1.8401 | |
| 274 | V | B | -1.0954 | |
| 275 | F | B | 0.0000 | |
| 276 | T | B | -0.9278 | |
| 277 | Q | B | -1.1747 | |
| 278 | D | B | -1.3419 | |
| 279 | E | B | 0.0000 | |
| 280 | W | B | 0.0000 | |
| 281 | L | B | -0.0690 | |
| 282 | K | B | -0.6145 | |
| 283 | F | B | 0.0000 | |
| 284 | E | B | 0.0000 | |
| 285 | Y | B | 0.0000 | |
| 286 | A | B | 0.0000 | |
| 287 | R | B | 0.0000 | |
| 288 | D | B | 0.0000 | |
| 289 | V | B | 0.0000 | |
| 290 | I | B | -0.4114 | |
| 291 | H | B | -0.6285 | |
| 292 | F | B | 0.0000 | |
| 293 | Y | B | 0.0000 | |
| 294 | R | B | -2.1816 | |
| 295 | A | B | -0.8875 | |
| 296 | G | B | 0.0000 | |
| 297 | P | B | -1.1226 | |
| 298 | G | B | 0.0000 | |
| 299 | N | B | 0.0000 | |
| 300 | P | B | 0.0023 | |
| 301 | Y | B | 0.3304 | |
| 302 | A | B | 0.0000 | |
| 303 | M | B | 0.1792 | |
| 304 | A | B | 0.0000 | |
| 305 | M | B | 0.1545 | |
| 306 | G | B | 0.0000 | |
| 307 | W | B | 0.0000 | |
| 308 | L | B | 0.0000 | |
| 309 | W | B | 0.0000 | |
| 310 | L | B | 0.0000 | |
| 311 | N | B | -0.9741 | |
| 312 | A | B | -0.9223 | |
| 313 | T | B | 0.0000 | |
| 314 | A | B | 0.0000 | |
| 315 | N | B | -1.9606 | |
| 316 | L | B | 0.0000 | |
| 317 | I | B | 0.0000 | |
| 318 | Q | B | -2.4627 | |
| 319 | K | B | -2.8774 | |
| 320 | G | B | -1.8741 | |
| 321 | P | B | -1.9052 | |
| 322 | E | B | -2.5790 | |
| 323 | A | B | -1.9499 | |
| 324 | G | B | -1.2257 | |
| 325 | P | B | -1.0180 | |
| 326 | V | B | 0.0000 | |
| 327 | F | B | 0.0000 | |
| 328 | L | B | 0.0000 | |
| 329 | S | B | 0.0000 | |
| 330 | F | B | 0.0000 | |
| 331 | G | B | 0.0000 | |
| 332 | H | B | -0.3996 | |
| 333 | D | B | -0.4408 | |
| 334 | G | B | -0.6552 | |
| 335 | D | B | -0.3626 | |
| 336 | I | B | 0.0000 | |
| 337 | I | B | 0.0000 | |
| 338 | P | B | 0.0000 | |
| 339 | M | B | 0.0000 | |
| 340 | L | B | 0.0000 | |
| 341 | A | B | 0.0000 | |
| 342 | A | B | 0.0000 | |
| 343 | L | B | 0.0000 | |
| 344 | G | B | -0.6033 | |
| 345 | L | B | 0.0000 | |
| 346 | F | B | -1.5668 | |
| 347 | D | B | -3.0763 | |
| 348 | D | B | 0.0000 | |
| 349 | E | B | -3.6891 | |
| 350 | K | B | -3.6556 | |
| 351 | K | B | -2.9402 | |
| 352 | L | B | 0.0000 | |
| 353 | P | B | -1.5148 | |
| 354 | T | B | -1.4432 | |
| 355 | D | B | -2.5299 | |
| 356 | E | B | -2.5523 | |
| 357 | V | B | -0.9074 | |
| 358 | Y | B | -0.7132 | |
| 359 | T | B | -0.8345 | |
| 360 | N | B | -1.7529 | |
| 361 | R | B | -2.5366 | |
| 362 | R | B | -2.9045 | |
| 363 | W | B | 0.0000 | |
| 364 | R | B | -1.0910 | |
| 365 | T | B | 0.0000 | |
| 366 | S | B | 0.0000 | |
| 367 | Q | B | -0.4885 | |
| 368 | I | B | 0.0000 | |
| 369 | V | B | 0.0000 | |
| 370 | P | B | 0.0000 | |
| 371 | M | B | 0.0000 | |
| 372 | G | B | 0.0000 | |
| 373 | G | B | 0.0000 | |
| 374 | R | B | 0.0000 | |
| 375 | I | B | 0.0000 | |
| 376 | L | B | 0.0000 | |
| 377 | L | B | 0.0000 | |
| 378 | Q | B | 0.0000 | |
| 379 | R | B | 0.0000 | |
| 380 | M | B | 0.0000 | |
| 381 | V | B | 0.1088 | |
| 382 | C | B | 0.0000 | |
| 383 | S | B | -0.7274 | |
| 384 | A | B | -1.1622 | |
| 385 | D | B | 0.0000 | |
| 386 | P | B | -1.9702 | |
| 387 | S | B | -1.6028 | |
| 388 | H | B | -2.3792 | |
| 389 | D | B | -2.7313 | |
| 390 | S | B | -1.9660 | |
| 391 | Q | B | -1.7944 | |
| 392 | A | B | -0.5421 | |
| 393 | G | B | -0.2461 | |
| 394 | V | B | -0.1653 | |
| 395 | F | B | 0.0000 | |
| 396 | I | B | 0.0000 | |
| 397 | R | B | 0.0000 | |
| 398 | F | B | 0.0000 | |
| 399 | N | B | 0.0000 | |
| 400 | V | B | 0.0000 | |
| 401 | N | B | 0.0000 | |
| 402 | D | B | -0.3785 | |
| 403 | G | B | 0.0000 | |
| 404 | I | B | 0.2286 | |
| 405 | V | B | 0.0000 | |
| 406 | A | B | -0.6821 | |
| 407 | L | B | 0.0000 | |
| 408 | P | B | -0.7415 | |
| 409 | G | B | -1.0430 | |
| 410 | C | B | -1.4606 | |
| 411 | D | B | -2.0395 | |
| 412 | S | B | -1.7392 | |
| 413 | G | B | 0.0000 | |
| 414 | P | B | -1.5429 | |
| 415 | G | B | -1.1115 | |
| 416 | E | B | -1.8833 | |
| 417 | S | B | 0.0000 | |
| 418 | C | B | 0.0000 | |
| 419 | P | B | -1.4969 | |
| 420 | L | B | -1.3141 | |
| 421 | D | B | -2.6536 | |
| 422 | R | B | -2.6883 | |
| 423 | L | B | 0.0000 | |
| 424 | M | B | -1.7565 | |
| 425 | A | B | -1.6972 | |
| 426 | H | B | -1.7796 | |
| 427 | V | B | 0.0000 | |
| 428 | A | B | -1.2481 | |
| 429 | E | B | -1.9521 | |
| 430 | R | B | -1.2209 | |
| 431 | G | B | -1.1630 | |
| 432 | S | B | -0.9330 | |
| 433 | M | B | 0.0417 | |
| 434 | G | B | -0.6277 | |
| 435 | G | B | -1.4395 | |
| 436 | D | B | -2.4965 | |
| 437 | F | B | -1.9069 | |
| 438 | R | B | -2.5174 | |
| 439 | K | B | -2.8116 | |
| 440 | T | B | -1.3508 | |
| 441 | C | B | 0.0000 | |
| 442 | G | B | -1.3771 | |
| 443 | L | B | -1.3517 | |
| 444 | P | B | -1.3715 | |
| 445 | E | B | -1.7909 | |
| 446 | W | B | -0.2207 | |
| 447 | A | B | 0.0000 | |
| 448 | P | B | -1.7033 | |
| 449 | D | B | -2.3577 | |
| 450 | R | B | -2.3855 | |
| 451 | L | B | -1.3562 | |
| 452 | T | B | -1.2033 | |
| 453 | F | B | -0.7572 | |
| 454 | L | B | -0.7371 | |
| 455 | R | B | -1.7098 | |
| 456 | Q | B | -1.7736 | |
| 457 | P | B | -1.1271 |
Calculations for various pH values
This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.
pH |
Average A4D Score |
Max A4D Score |
|||
| 4.0 | -0.5181 | 3.6473 | View | CSV | PDB |
| 4.5 | -0.5879 | 3.4412 | View | CSV | PDB |
| 5.0 | -0.6734 | 3.2708 | View | CSV | PDB |
| 5.5 | -0.7597 | 3.2012 | View | CSV | PDB |
| 6.0 | -0.8322 | 3.1357 | View | CSV | PDB |
| 6.5 | -0.8807 | 3.0825 | View | CSV | PDB |
| 7.0 | -0.9053 | 3.0445 | View | CSV | PDB |
| 7.5 | -0.9136 | 3.0172 | View | CSV | PDB |
| 8.0 | -0.9125 | 2.9954 | View | CSV | PDB |
| 8.5 | -0.9035 | 2.9773 | View | CSV | PDB |
| 9.0 | -0.8852 | 2.9648 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine